When I was a little boy I loved the funny papers. ... I used to read Pogo, Li'l Abner, Peanuts, Blondie and B.C. among others. I loved to draw Johnny Hart's B.C. characters and the Muppets. I made up my own cartoon characters and drew stories about them. I loved Mad magazine. I had paperback reprints of the early [Harvey] Kurtzman stories, illustrated by Wally Wood, Will Elder, and Jack Davis. I loved Disney movies. ... I would come home from the movies and practice drawing the characters. I drew little animated flip books on index cards. When I was 11, I had a Super-8 movie camera and I made animated cartoons. I remember making a 'King Kong' out of clay, and a drawing of a New York skyline, and I made a stop-motion film of King-Kong fighting model airplanes. In junior high school, I drew comic books and Xeroxed them at my dad's office. I sold the Xeroxes for five cents each. I think I made fifteen cents.[4]

Baker's first credited work at Marvel is penciling the half-page entry "Kid Commandos" in The Official Handbook of the Marvel Universe #13 (Feb.1984).[7] After a handful of inking assignments on issues of Transformers, The Avengers Annual #14 (1985) and elsewhere, Baker made his professional story-illustration debut as penciler and inker of the publisher Lodestone Comics' Codename: Danger #2 (Oct. 1985), with a 23-page story written by Brian Marshall, Mike Harris, and Robert Loren Fleming. Cover penciling and more interior inking for Marvel and occasionally DC followed. His first story penciling for one of the two major comics companies was the three-issue Howard The Duck: The Movie (Dec. 1986 - Feb. 1987), adapting the 1986 film Howard the Duck, and which he self-inked.[7]

During this time, Baker also attempted to sell humor spot illustrations, but was rejected by the major newspapersyndicates. Jim Salicrup, a Marvel editor, did commission him "to write a few one-panel gags about [the superhero team] the X-Men",[4] titled "It's Genetic" and appearing in the Marvel-produced fan magazine Marvel Age.[8]

At the recommendation of freelance artist Ron Fontes, an editor at the Dolphin imprint of the publishing house Doubleday expressed interest in Baker's sample strips of the character Cowboy Wally, "and asked if I had any more. I lied and said I did."[4] This led to the 128-page graphic novelCowboy Wally.[7] "The character of Noel was pretty much based on me," Baker said in 1999. "I lie all the time.[9] The first part of the books is the collected strips, and the other three chapters were written for the book.[4] "It didn't sell many copies," Baker said, "but at least it convinced DC [Comics] I should be allowed to draw, not just ink."[4]

He began scripting comics around this time: Baker penciled and inked First Comics' Classics Illustrated #3 & 21 (Feb. 1990 & March 1991), adapting, respectively, Through the Looking Glass and Cyrano de Bergerac. While Peter David scripted the latter, Baker himself wrote the adaptation of the Lewis Carroll work.[7] "I'd never planned to become a writer," Baker said in 1999. "I wrote short gags, like the kind you see in the newspapers and Cowboy Wally, but not stories. I only learned to write stories because people kept paying me to write them. In the years 1991-1994, 90 percent of my income was from writing, and I received very few offers to draw. I figured I should learn to write."[4]

Baker achieved recognition and won an Eisner Award for his 1990 graphic novel Why I Hate Saturn, published by the DC Comics imprintPiranha Press. Baker said in 1999 of his breakthrough work,

I wrote Why I Hate Saturn at a time when comic books had stopped being fun for me. I was tired of being told how to draw and what to draw. And I was sick of begging people to let me work the way I wanted. Editors told me my stuff was 'underground' and 'alternative'. I decided that if I were going to work in a creatively oppressive atmosphere and not even be allowed to own my work, I might as well go to Hollywood and be oppressed for big money. Back in the eighties, DC and Marvel wouldn't let you own your characters, and Fantagraphics had no money. So when I finally got permission to do Why I Hate Saturn, a book I'd been trying years to sell, I decided to write it like a sitcom and send it to Hollywood. ... [However,] I don't have anything to do with the [then-proposed] Why I Hate Saturn movie. DC controls those rights. I don't own those characters, so it is of no interest to me.[4]

At this point in his career, Baker stated in an interview, "Nobody tells me what to write or how to draw. Only an idiot would dare tell Kyle Baker how to make a good cartoon. Hollywood and the magazine world are full of idiots. They water my stuff down and make it unfunny."[9]

He is credited with writing and storyboarding on the "Phineas and Ferb" television episodes "Candace Loses Her Head" and "Are You My Mummy?".[citation needed]

In 2006, his company, Kyle Baker Publishing, serialized a four-part comic book series about Nat Turner, and published the series The Bakers, based on his family life, in two anthologies, Cartoonist and Cartoonist Vol. 2: Now with More Bakers. He has also continued to provide comics material sporadically to Marvel, DC and Image Comics through at least 2010.[7] In 2007 and 2008, Image Comics published Baker's six-issue Image Comics miniseries Special Forces, a teen-soldier military satire that criticizes the exhortation of felons and disabled Americans into military service.[7][12]The New York Times reviewed the 2009 trade-paperback collection of the first four issues, calling it "the harshest, most serrated satire of the Iraq War yet published."[13]